Ok, I've made an ent file to fix the issue. Test it and make sure it's no longer possible to get through the window.
This bug is rather interesting. I must have changed something somewhere. In Quake2 when you crouch and step off of something, you stand up again. I remember crouching down hills and bouncing up and down because the game kept popping between crouched and standing. I don't remember changing this, but apparently now you can crouch down hills, down stairs, and off ledges without popping back into an upright pose. Now I'm wondering what I did, and in what version the change took place. I also wonder what animation it plays.